A quantitative trait locus (QTL) is a site on a chromosome containing genes (alleles) influencing a quantitative or multilocus trait. In our present RO1 grant, QTL analysis was used to detect and map ten QTLs influencing either acute or chronic alcohol (EtOH) withdrawal severity to broad chromosomal regions using crosses between the C57BL/6 (B6) x DBA/2 (D2) and the Withdrawal Seizure Prone (IP2) x Withdrawal Seizure Resistant (IR1) inbred strains. The gene has been identified which accounts for one of these, and good progress toward this end has been made for another. In this proposal we plan to advance toward gene identification for the seven QTLs focused on the chronic alcohol withdrawal model in B6xD2 and IP2xlR1 crosses rather than the acute model used in the past. The approach is to combine gene expression microarray and QTL data taken in the same mice to take full advantage of the complementary strengths and weaknesses of these two genome-wide methods of gene discovery. Recent work has shown that individual variation in gene expression in brain for most genes, as indexed by transcript (mRNA) abundance, is often controlled by multiple loci (QTLs). By combining microarray and QTL (quantitative trait locus) analysis on the same mice, we propose to detect those transcripts most likely to have a direct influence oh withdrawal severity by determining which transcripts segregate with withdrawal variation and which do not, and also which QTLs jointly influence variation in transcript abundance for particular gene(s) and withdrawal severity. We will use short-term selected lines bred for high and low chronic alcohol withdrawal severity to verify differential gene expression for candidate genes cosegregating with withdrawal severity. Analyses of specialized high resolution mapping populations of congenic strains, haplotype analyses, and analyses of gene function will provide increasing differentiation among candidate genes which will contribute importantly toward the identification of those genes responsible for the seven known QTLs influencing chronic alcohol withdrawal severity. Another major focus of these studies is to determine the effects of chronic intoxication, either with or without withdrawal, on gene regulation throughout the genome, as this will provide important clues concerning mechanism. We will use the newly available Affymetrix mouse 430 2.0 Genechip(r) representing the vast majority of all genes in the mouse genome. [unreadable] [unreadable]